Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to...

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Fakultät für Chemie und Biochemie Modulhandbuch Master of Science (MSc) in Molecular Sciences and Simulation

Transcript of Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to...

Page 1: Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets,

Fakultät für Chemie und Biochemie

Modulhandbuch Master of Science (MSc) in

Molecular Sciences and Simulation

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Curriculum: Sem. Nr. Module V Ü/S Pr Type CP Responsible 0. L Leveling Course in Mathematics 2 2 optional Servicezentrum

Mathematik E Scientific English for non-native speakers 2 2 optional Language

Center (ZFA) 1. 1 Basic Concepts of Quantum Mechanicsa 2 1 EC 5 Physics 2 Statistical Physics and Thermodynamicsa 2 1 EC 5 ICAMS 3 Simulation and Dynamics 2 1 4 RC 9 ThC 4 Concepts of Spectroscopy 1 2 1 5 RC 9 PC/PTT 5 Concepts of Molecular Chemistry 1 2 1 RC 5 AC/OC 24 wch 10 5 9 28/33 2. 6 Electronic and Molecular Structure 2 1 5 RC 9 ThC 7 Concepts of Spectroscopy 2 2 1 4 RC 9 PC/TeC 8 Concepts of Molecular Chemistry 2 2 1 RC 5 AC/OC 9 Theoretical Spectroscopy 2 1 RC 5 ThC 10 Numerical Methods and Scientific Computinga 2 1 EC 5 Servicezentrum

Mathematik 21 wch 8 4 9 28/33 3. 11 International Course 14 RC 14 International

Partners 12 Focal Point Practical 15 RC 15 Participating

groups 29 wch 2 2 25 29 4. 13 Masters Thesis RC 30 Participating

groups 74 wch 20 11 43 120 aVon den drei Modulen Basic Concepts of Quantum Mechanics, Statistical Physics and Thermodynamics und Numerical Methods and Scientific Computing sind mindestens zwei zu belegen. Die auf den Studiengang speziell zugeschnittenen Vorkurse werden im September vor Semesterbeginn stattfinden. Erläuterungen: V: Vorlesung, Ü/S: Übung/Seminar, Pr: Praktikum, CP: credit points, RC: Pflichtveranstaltung (required course), EC: Wahlpflichtveranstaltung (elective course), wch: Semesterwochenstunden (weekly contact hours). Die Vorlesungszeit umfasst im Wintersemester 15 Wochen, im Sommersemester 13 Wochen. Die fettgedruckten Kurse: neu oder signifikant weiterentwickelt. Beteiligte:

1. ThC: Theoretische Chemie (Marx, Hättig) 2. PC: Physikalische Chemie (Havenith-Newen, Herrmann, Weingärtner, N.N.) 3. OC: Organische Chemie (Sander) 4. AC: Anorganische Chemie (Fischer, Mudring) 5. TeC: Technische Chemie (Muhler) 6. PTT: Fakultät für Elektrotechnik: Photonik und Terahertztechnologie (Hofmann) 7. Fakultät für Physik/ICAMS (Drautz, N.N., Czarnetzki)

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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title of module Module M: Leveling Course in Mathematics

credit points available in semester(s) 0

hours per week compact course

lecturer(s) Lecturer of the Servicezentrum Mathematik und Anwendungen (SZMA), person in charge: Hättig

teaching methods

lectures and exercise sessions

evaluation of learning progress

active participation during lecture and exercise sessions, homework corrected by teaching assistant, presentation of solutions in exercise sessions

mode of examination

learning objectives students will consolidate their knowledge about basic mathematical methods and gain routine in applying mathematical methods for the solution of scientific problems

soft skills

note-taking during lectures, independent post-preparation of module contents, consultation of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module Matrix and operator calculus: solution of eigenvalue problems for matrices and operators with focus on symmetric or hermitian matrices/operators, unitary matrices/operators, transformations between different basis sets, functions of matrices and operators Differential equations (DE): basic concepts and definitions, classification of DEs and their solutions, standard approaches for the solution of some common types of DE, variation of constants, systems of DEs, application of DEs to e.g. vibrations, chemical kinetics, quantum mechanics Statistics: probability distributions (binomial, normal, Poisson, boltzmann, etc. distributions), averages and standard deviations, regression, data analysis, confidence intervals and hypothesis testing.

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FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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title of module Module E: English for Non-Native Speakers

credit points available in semester(s) 0

hours per week compact course

lecturer(s) Lecturer of the ZfA, person in charge: Heimann-Bernoussi

teaching methods

lectures and exercise sessions

evaluation of learning progress

active participation during lecture and exercise sessions, interactive correction of oral and textual contributions

mode of examination

learning objectives Students will consolidate their basic English knowledge, improve their language skills with an emphasis on technical terms required for the master course program and will gain routine in applying spoken and written English to situations common in science such as oral presentations and written reports.

soft skills

note-taking during lectures, independent post-preparation of module contents, active communication in foreign language

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contents of module Language skills: consolidation of language skills based on IELTS level 6.0 or better, improvement of active and passive vocabulary, broadening of technical vocabulary relevant for the master course program and application to everyday scientific situations. Presentation techniques: basic concepts and practical application to realistic scenario (conference presentation) Scientific Writing: basic concepts and practical examples (e.g. lab report, scientific paper).

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title of module Module 1: Concepts of Quantum Mechanics

credit points 5 available in semester(s) 1

hours per week 3 compact course

lecturer(s) Institute of Theoretical Physics at RUB, person in charge: Marx

teaching methods

lecture: 2 hours per week exercises: 1 hour per week

evaluation of learning progress

active participation during lectures, weekly homework corrected by teaching assistant and/or interactive presentation of homework during exercises

mode of examination 30 - 45 min end-of-term oral exam or 2-hour end-of-term written exam

learning objectives students acquire advanced knowledge on selected topics of concepts and techniques of quantum mechanics and quantum statistical mechanics as needed in the realm of (bio)molecular systems such as molecules, clusters, liquids, solids and surfaces. This knowledge will be necessary to better understand dynamics and simulation, electronic and molecular structure, and theoretical spectroscopy of aforementioned systems.

soft skills

notetaking during lectures, independent post-preparation study of module contents and reading of relevant literature; interactive presentation in front of an audience

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module introduction to/motivation of quantum mechanics (2h) review of basic quantum mechanics: real-space and momentum-space representation, Hilbert space concept and bra/ket notation (2h) harmonic oscillator: algebraic solution, ladder operators (2h) Pauli principle and antisymmetrization of wavefunction, spin/orbital angular momenta and their coupling (4h) non-degenerate time-independent perturbation theory, variational principle (Rayleigh-Ritz), Hartree Fock (4h) time-dependent quantum mechanics: Schrödinger, Heisenberg and Dirac picture, time-dependent Schrödinger equation, Heisenberg equation of motion, time evolution operator, propagator/Green function concept (4h) time-dependent perturbation theory: intermediate/interaction picture, transition probabilities, constant and periodic perturbations, sudden approximation (4h) introduction to quantum-statistical mechanics: statistical/density operator, thermal density matrices, quantum-statistical expectation values, statistical mixtures and pure states, thermal Boltzmann operator, restricted summation for identical particles, classical limit, interpretation of canonical partition function as path integral, basic ideas of path integral formalism of quantum mechanics and quantum-statistical mechanics: time-dependent propagator, free particle solution, thermal propagator (Feynman-Kac) and connection to statistical mechanics (6h) The total student work load is 150 hours, total contact hours: 45

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title of module Module 2: Statistical Physics and Thermodynamics

credit points 5 available in semester(s) 1

hours per week 3 compact course

lecturer(s) lecturers from ICAMS, person in charge: Steinbach

teaching methods

lecture: 2 hours per week seminar & group work: 1 hour per week

evaluation of learning progress

active participation during lectures, weekly homework corrected by teaching assistant, interactive presentation of homework during exercises

mode of examination written examination

learning objectives Students gain knowledge about the fundamental concepts of equilibrium thermodynamics and statistical mechanics; enabling the students with engineering background to understand the basic physical concepts and develop the skills in applying these concepts to materials modelling and solid state physics.

soft skills

interactive presentation in front of an audience, notetaking during lectures, independent post-preparation of module contents, independent consultation of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module • Introduction to key concepts of probability theory: probability distributions, expectation values, central limit theorem • Physical concepts in classical mechanics required for the understanding of statistical mechanics • Basic concepts in classical thermodynamics: state variables, thermodynamic functionals, entropy, extremal principles, Legendre transformations, Maxwell relations, phase equilibria, Clausius-Clapeyron equation, ideal gas, reversibility and irreversibility, adiabatic processes • Linking classical mechanics to statistical mechanics: microcanonical, canonical and grand canonical ensemble, equipartition theorem, Maxwell distribution • Basic aspects of quantum statistics Total student work load: 150 hours Contact time: 45 hours

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title of module Module 3: Dynamics and Simulation

credit points 9 available in semester(s) 1

hours per week 8 compact course

lecturer(s) D. Marx, N.N., person in charge: D. Marx

teaching methods

lecture: 2 hours per week, exercises: 1 hour per week, integrated practial: 5 hours per week

evaluation of learning progress

active participation in lecture and practical, presentation of homework during exercises, feedback during and on virtual experiments, written homework and lab reports

mode of examination 30 - 45 min end-of-term oral exam or 2-hour end-of-term written exam

learning objectives students acquire advanced knowledge on the theory and techniques of statistical mechanics and (bio)molecular dynamics in the realm of (bio)molecular systems such as (bio)molecules, clusters, liquids, solids and surfaces. In addition, analysis methods to extract observables of experimental interest, such as various spectroscopic, scattering, and diffraction techniques, are presented such that the students can judge both their strenghts and weaknesses with the focus on (bio)molecular condensed matter systems

soft skills

notetaking during lectures, independent post-preparation study of module contents and reading of the relevant literature; interactive presentation in front of an audience

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module essentials of classical and statistical mechanics: formulations according to Newton, Lagrange and Hamilton, corresponding equations of motion, conservation laws/conserved quantities, Liouville theorem, ensembles, distribution functions, first and second moments of distributions, connection to averages and fluctuations of observables, correlation functions in space and time, pair and radial correlation function, van Hove correlation function potential energy surfaces: valence force fields, pair potentials, many-body effects, empirical versus ab initio parameterizations, characterization of stationary points, connection between properties of hypersurfaces and chemical concepts, adiabatic chemical reactions molecular dynamics: basic idea of classical molecular dynamics, deriving integrators via "pedestrian approach" and via Liouville formalism, ergodicity, extended phase space/Lagrangian methods, finite-size effects, boundary conditions, convergence criteria for dynamical computer simulations, realizing various ensembles in terms of simulation algorithms, holonomic constraints, ab initio molecular dynamics, equations of motion according to Ehrenfest, Born-Oppenheimer and Car-Parrinello integrated practial work in the computer lab will closely follow the theoretical discussion during the lecture and will supplement the analytical exercises (homework). In particular, structure, dynamics and properties of selected (bio)molecular condensed phase systems at finite temperatures and subject to periodic boundary conditions, such as molecular liquids, solutions, and solvated biomolecules, will be in the focus of the virtual experiments. Total student work load: 270 hours Contact time: 120 hours

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title of module Module 4: Concepts of Spectroscopy 1

credit points 9 available in semester(s) 1

hours per week 8 compact course

lecturer(s) M. Havenith, N.Yukam, E. Sanchèz-García, person in charge: M. Havenith

teaching methods

lecture: 2 hours per week exercises: 1 hour per week practicals: 5 hours per week

evaluation of learning progress

active participation during lectures, weekly written short tests (15min), homework corrected by teaching assistant, interactive presentation of homework during

i

mode of examination 2-hour end-of-term written exam

learning objectives The course aims to provide theoretical and practical knowledge on modern linear and nonlinear spectroscopic methods (time- and frequency domain) which allow for the elucidation of molecular structure and dynamics in different environments. The course material covers the application of single-, double- and triple-resonance laser spectroscopic techniques from the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets, rare gas matrices, the liquid phase and at interfaces. The accompanying lab course is intended to foster the practical understanding of the lase spect oscopic techniq es and thei application in

soft skills

interactive presentation in front of an audience, notetaking during lectures, independent post-preparation study of module contents and reading the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module 1. The electromagnetic spectrum, theory of generation and properties of ns, ps, and fs laser pulses, tunable pulsed and cw lasers, pulse duration, spectral bandwidth, Fourier transformation. 2. Line broadening mechanisms and their removal: rare gas matrix, supersonic jet expansion, molecular beam, Helium nanodroplet. 3. Molecular symmetry, point groups, molecular symmetry groups. 4. Rotational spectroscopy: linear, symmetric, spherical, and asymmetric rigid rotor molecules, rotational infrared, millimeter, microwave spectra, structure determination from rotational constants, determination of conformational geometries. 5. Vibrational spectroscopy: diatomic and polyatomic molecules, infrared and Raman spectra, vibrational selection rules, normal mode analysis (Wilson FG matrix method), effective and exact molecular Hamiltonians, double resonance techniques, intramolecular vibrational redistribution (IVR). 6. Electronic spectroscopy: diatomic and polyatomic molecules, electronic and vibronic selection rules, one- and multi-dimensional Franck-Condon analysis, intramolecular nonradiative processes (internal conversion, intersystem crossing), curve crossings and conical intersections. Frequency domain methods (e.g. LIF), Transition State spectroscopy (negative ion photodetachment), velocity map ion imaging. 7. Photoelectron spectroscopy: ionization process and Koopmans' theorem, molecular UV photoelectron spectra in the frequency-domain, Franck-Condon analysis, ZEKE spectroscopy. Total student work load: 240 hours Contact time: 120 hours

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title of module Module 5: Concepts of Molecular Chemistry 1

credit points 5 available in semester(s) 1

hours per week 3 compact course

lecturer(s) W. Sander, N.N.; person in charge: W. Sander

teaching methods

lecture: 2 hours per week exercises: 1 hour per week

evaluation of learning progress

active participation during lectures, homework corrected by teaching assistant, interactive presentation of homework during exercises, 20 min presentation of a scientific paper

mode of examination 30 min end-of-term oral exam

learning objectives Students acquire basic knowledge on molecular reactivity and the concepts of physical organic chemistry such as properties related to electron density and potential energy surfaces. They learn to estimate the thermodynamics and kinetics of chemical reactions from simple concepts such as additivity rules, and to evaluate the experimental basis of such rules.

soft skills

interactive presentation in front of an audience, notetaking during lectures, unsolicited post-preparation of module contents, unsolicited consultation of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module Concepts of covalent and non-covalent bonds, thermodynamics and kinetics of chemical reactions, potential energy surfaces, the basis of force field calculations, Benson additivity rules, linear free energy relationships Total student work load: 150 hours Contact time: 45 hours

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title of module Module 6: Electronic and Molecular Structure Theory

credit points 9 available in semester(s) 2

hours per week 8 compact course

lecturer(s) C. Hättig; person in charge: C. Hättig

teaching methods

lectures: 2 hours per week exercises: 1 hour per week practicals: 5 hours per week

evaluation of learning progress

active participation, homework corrected by teaching assistant, presentation and discussion of homework and results from practicals in exercise session

mode of examination 30 - 45 min end-of-term oral exam

learning objectives Students acquire advanced knowledge of electronic and molecular structure theory and quantum chemical methods and how these methods can be applied to solve typical problems e.g. in thermochemistry, spectroscopy, or structure determination. Furthermore they will learn how to judge the accuracy and reliability of methods and how to analyse and present results of electronic and molecular structure calculations.

soft skills

interactive presentation in front of an audience, note-taking during lectures, independent post-preparation of module contents, consultation of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module Many-electron wavefunctions: quantum mechanical description of many-particle systems, Pauli principle, Slater determinants, matrix elements for Slater determinants and many-electron wavefunctions Second quantization (particle number representation): Fock space and occupation number vectors, creation and annihilation operators, representation of one- and two-electron interactions in second quantization, representation of excited determinants, spin free operators Self-consistent field (SCF) and multi-configurational self-consistent field (MCSCF) methods: Hartree-Fock and coupled perturbed Hartree-Fock equations in second quantization, solution of HF equations, exponential parameterization of unitary transformations, MCSCF methods as e.g. CASSCF and RASSCF, choice and validation of active spaces Multi-reference correlation methods: multi-reference perturbation theory, CASPT(2), multireference CI, internally and externally contracted variants, construction of the many-particle basis functions Coupled-Cluster methods: the coupled-cluster wavefunction ansatz and its properties, the projected Schrödinger equation, size-consistency, the standard coupled-cluster models, perturbative triples corrections, CCSD(T) Explicitly-correlated F12 methods: static and dynamic correlation, explicitly correlated wavefunctions, R12 ansatz of Kutzelnigg, modern F12 methods, MP-F12 and CCSD-F12 Efficient methods for large systems: direct methods, integral screening and approximations Application of quantum chemical methods to typical problems, e.g. structure optimization, ionization energies, electron affinities, UV and CD spectra, IR and Raman spectra, reaction and activation energies, entropies, enthalpies and free enthalpies. Basis set convergence and accuracy of quantum chemical methods, additive correction schemes. Total student work load: 240 hours Contact time: 120 hours

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title of module Module 7: Concepts of Spectroscopy 2

credit points 9 available in semester(s) 2

hours per week 8 compact course

lecturer(s) K. Morgenstern, M. Havenith; person in charge: M. Havenith

teaching methods

lecture: 2 hours per week exercises: 1 hour per week practicals: 5 hours per week

evaluation of learning progress

active participation during lectures, homework corrected by teaching assistant, interactive presentation of homework during exercises

mode of examination 2-hour end-of-term written exam

learning objectives Students learn spectroscopic techniques to investigate biomolecular structure, dynamics and interactions. The accompanying lab course is intended to foster the practical understanding of spectroscopic methods using biomolecular model systems. Students are integrated in ongoing research projects through an hands-on approach.

soft skills

interactive presentation in front of an audience, notetaking during lectures, unsolicited post-preparation of module contents, unsolicited consultation of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module 1. Optical Properties of molecules: Interaction of molecules with light across the electromagnetic spectrum; Linear IR and UV/VIS spectroscopy with biomolecular examples 2. Basic Fluorescence Techniques: measurement techniques, quantum yield and lifetime, fluorescence extinction and depolarisation, FRAP 3. Chiroptical Spectroscopy: Optical rotatory dispersion, Circular dichroism 4. Single Molecule Spectroscopy: Optical single molecule spectroscopy, Fluorescence correlation spectroscopy 5. Ultrafast- and Nonlinear Spectroscopy: Multiphoton excitation, ultrafast spectroscopy, pump-probe techniques 6. In-Cell Techniques: NMR spectroscopy, mass spectrometry, FCS, single particle tracking 7. Microscopy Techniques: electron microscopy (TEM/SEM), scanning probe microscopy Total student work load: 240 hours Contact time: 120 hours

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title of module Module 8: Concepts of Molecular Chemistry 2

credit points 5 available in semester(s) 2

hours per week 3 compact course

lecturer(s) A.-V. Mudring, R. Schmid; person in charge: A.-V. Mudring

teaching methods

lecture: 2 hours per week exercises: 1 hour per week

evaluation of learning progress

active participation during lectures,homework corrected by teaching assistant, interactive presentation of homework during exercises

mode of examination 2-hour end-of-term written exam

learning objectives Students acquire advanced knowledge on the interpretation of the electronic structure of organic and inorganic molecular compounds and systems of higher dimensionality. They learn quantitative means electronic structure interpretation.

soft skills

interactive presentation in front of an audience, notetaking during lectures, independent post-preparation study of module contents and reading of the relevant literature

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module Symmetry and topology Intermolecular interactions -Calculation and experimental determination of electron densities in molecular compounds, of surfaces and of solids. -Concepts of topological interpretation of electron density like AIM and ELF; NBO, Mulliken population, Edminston-Rüdenberg localization, Wannier orbitals -Weak interactions: Host-guest interactions, adsorbates on surfaces, hydrogen bonding, pi-interactions -Reactions at surfaces -Reactive intermediates Total student work load: 150 hours Contact time: 45 hours

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title of module Module 9: Theoretical Spectroscopy

credit points 5 available in semester(s) 2

hours per week 3 compact course

lecturer(s) D. Marx, N.N; person in charge: D. Marx

teaching methods

lecture: 2 hours per week exercises: 1 hour per week

evaluation of learning progress

active participation during lectures, weekly homework corrected by teaching assistant and/or interactive presentation of homework during exercises

mode of examination 30 - 45 min end-of-term oral exam or 2-hour end-of-term written exam

learning objectives students aquire knowledge on theoretical approaches relying on time-dependent methods to compute observables which are obtained experimentally using spectroscopic, scattering, and diffraction techniques. The students will be able to judge both scope and limitations of such methods with a focus on (bio)molecular condensed phase systems, in particular liquids and soft matter

soft skills

notetaking during lectures, independent post-preparation study of module contents and reading of the relevant literature; interactive presentation in front of an audience

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module ingredients from quantum dynamics: time-dependent variational principle (Dirac-Frenkel), linear TDVP, Gaussian wavepaket propagation methods (Heller, Singer), exact wavepaket propagation methods (relying e.g. on split-operator dual-space representation, Chebyshev expansion, second-order differencing, Krylov subspace / Lanczos methods) time-dependent perturbation theory: formalism and applications to schematic models, linear TDVP in interaction picture, first- and second-order diagrams, virtual states/transitions, Fermi’s Golden Rule, molecular systems in the radiation field: transition probability, absorption cross section, dipole approximation, transition dipole, semiclassical approach and basics of electromagnetic field quantization (spontaneous emission), multi-photon processes, transformation of spectroscopy in Schrödinger picture and to Heisenberg picture (Kubo-Gordon formalism), time autocorrelation functions and spectral line shape function neutron scattering and x-ray diffraction: van Hove formalism, Born approximation, Fermi contact potential, dynamics and static structure factor, scattering length and form factors, coherent and incoherent scattering, van Hove correlation function and the structure and dynamics of liquids, pair correlation function, radial distribution function Total student work load: 150 hours Contact time: 45 hours

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title of module Module 10: Numerical Methods and Scientific Computing

credit points 5 available in semester(s) 2

hours per week 3 compact course

lecturer(s) Hättig, Schmid, person in charge: Hättig

teaching methods

Lectures and exercise sessions

evaluation of learning progress

active participation during lectures, homework corrected by teaching assistant, presentation of solutions during exercises

mode of examination 30 - 45 min end-of-term oral exam or 2-hour end-of-term written exam

learning objectives The module is designed as a first course in applied mathematics and scientific computing. Students will get a basic knowledge of numerical methods and algorithms for solving typical problems in natural sciences, the implementation of such algorithms in a computer language and how to judge the accuracy and reliability of numerical methods.

soft skills

note-taking during lectures, presentation of result to an audience, writing, compiling and testing computer programs

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module The course will introduce into state-of-the-art scientific programming languages and applications to numerical problems in chemical sciences: Fortran90, a language for high-performance computing: data types, storage of arrays (vectors, matrices, etc.) user-defined data types, subroutines, functions and modules, in- and output of data Python: a modern object-oriented programming language used in many scientific codes, high-level data types, how to make use of object orientation Scientific Subroutine Libraries: BLAS (Basic Linear Algebra Package), LAPACK (Linear Algebra Package) NumPy/Scipy: using the numerical extensions of Python for efficient computing, data processing and analysis Solving standard numerical problems: - linear equations and least square fits - eigenvalue problems: power iteration, Rayleigh quotient iteration, Lanzcos and Davidson methods - numerical integration: Euler, Verlet, Runge-Kutta, and Numerov method - periodic boundary conditions Cost analysis, efficiency and optimization Hands-on training at prototype examples such as the development of programs for Hückel calculations, molecular dynamics or the numerical solution of one-dimensional Schrödinger equations. Total student work load: 150 hours Contact time: 45 hours

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title of module Module 11: International Course

credit points 14 available in semester(s) 3

Student work load 420 compact course

lecturer(s) Faculty of the partner universities of the Master Program Molecular Sciences and Simulation,

teaching methods

research oriented lab project (6 weeks full-time or equivalent) in one of the research groups

evaluation of learning progress

active participation in practical, feedback during and on the experiment, feedback on written lab report by teaching assistants

mode of examination the project has been completed successfully and written up satisfactorily in a lab report

learning objectives advanced knowledge of the application of computational and/or experimental methods employed in state-of-the-art research in order to understand the properties of (bio)molecular systems, critical assessment of the scope and limitations of various approaches/approximations, visualization and presentation of results

soft skills

international teamworking and collaboration, graphical presentation of practical results, general knowledge of experimental and computational methods, acquaintance with alternative work flow organisation

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

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contents of module The practical is carried out in a research group located at one of our international partner universities/scientific institutions. The student will learn methods complementory to those available at Ruhr University Bochum. The student is expected to extend her/his experimental/theoretical skills to techniques not available in Bochum or to apply skills gained in Bochum to research topics in the hosting group. Typical contact time: 300 hours

Page 32: Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets,

title of module Module 12: Focal Point Practical

credit points 15 available in semester(s) 3

Student work load 450 compact course

lecturer(s) Faculty of the Master Program Molecular Sciences and Simulation

teaching methods

research oriented lab project (e.g. 6 weeks full-time or equivalent) in one of the research groups

evaluation of learning progress

active participation in practical, feedback during and on the experiment, feedback on written lab report by teaching assistants

mode of examination the project has been completed successfully and written up satisfactorily in a lab report

learning objectives advanced knowledge of the application of computational and/or experimental methods employed in state-of-the-art research in order to understand the properties of (bio)molecular systems, critical assessment of the scope and limitations of various approaches/approximations, visualization and presentation of results

soft skills

teamworking and collaboration while carrying out project, graphical presentation of practical results, general knowledge of experimental and computational methods

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

Page 33: Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets,

contents of module The practical is carried out in one or several groups participating in the Master of Molecular Sciences and Simulation program. Examples of elective project topics: Marx group portfolio: force field simulation of peptides in water: hydrophilic vs. hydrophobic solvation, Car-Parrinello simulation of de/protonation reactions in explicit solvent computation, decomposition and assignment of infrared spectra of molecules in solution Sander/Mudring/Schmid portfolio: The students will learn to characterize reactive molecules by low temperature (matrix isolation) and time resolved spectroscopy in combination with quantum chemical (DFT and ab initio) calculations. Hättig portfolio: computation of UV and CD spectra and investigation of excited states, energetics and structure of weakly interacting complexes, computation of reaction and activation enthalpies, computer implementation of quantum chemical methods Havenith/Müller/Ebbinghaus/Weingärtner portfolio: study the interaction of small molecules by helium droplet spectroscopy, investigate solute-solvent interactions for aqueous solutions of molecular compounds in the THz and other spectral ranges, use different microscopic techniques to study and chemically map surfaces at nanoscale contact time: typically 250 hours

Page 34: Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets,

title of module Module 13: Master Thesis

credit points 30 available in semester(s) 4

Student work load 900 compact course

lecturer(s) Faculty of the Master Program Molecular Sciences and Simulation

teaching methods

active supervision: regular progress meetings, supervised presentation of project and results.

evaluation of learning progress

Feedback on progress meeting reports, feedback during and on (computer) experiments.

mode of examination Required is a written report (50-100 pages typical) describing in detail the project and its results

learning objectives Students acquire the ability to plan, organize, develop, operate and present complex problems in Molecular Sciences and Simulation (MOS). The master thesis qualifies students to work independently in a MOS subject under the supervision of an advisor. The students’ are able to deal with subject-specific problems and to present them in an appropriate and comprehensible manner and according to scientific standards. They have acquired the profound specialised knowledge, which is required to take the step from their studies to professional life..

soft skills

interdisciplinary teamworking and collaboration while carrying out project, graphical presentation of complex topics, detailed knowledge of experimental and computational methods.

FAKULTÄT FÜR CHEMIE UND BIOCHEMIE Master Program Molecular Sciences and Simulation

Page 35: Modulhandbuch Master of Science (MSc) in Molecular ... · the THz to the VUV wavelength region to the study of molecules and their interactions in molecular beams, Helium nanodroplets,

contents of module The master thesis can be theoretically and/or practically oriented. Its topic is determined by the respective supervisor. Typical contact time: 700 hours